@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/commonjs/RcsbQueries/Borrego/schema.graphql

@@ -1,412 +0,0 @@
-# This file was generated based on ".graphqlconfig". Do not edit manually.
-
-schema {
-    query: Query
-}
-
-type AdditionalProperty {
-    """
-
-    The additional property name.
-
-    Examples:
-    PARENT_COMP_ID, CATH_NAME, PARTNER_BOND_DISTANCE
-    """
-    property_name: PropertyName
-    property_value: [ObjectScalar]
-}
-
-type AlignedRegion {
-    "List of genomic indexes that are needed to complete the last nucleotide triad of a genome-protein sequence alignment"
-    exon_shift: [Int]
-    "Query sequence start position"
-    query_begin: Int!
-    "Query sequence end position"
-    query_end: Int!
-    "Target sequence start position"
-    target_begin: Int!
-    "Target sequence start position"
-    target_end: Int!
-}
-
-type AlignmentLogo {
-    symbol: String
-    value: Int
-}
-
-type AlignmentResponse {
-    "Length of the alignment"
-    alignment_length: Int
-    alignment_logo: [[AlignmentLogo]]
-    "Full sequence of the query"
-    query_sequence: String
-    "JSON schema that describes the different alignments between the query sequence and targets"
-    target_alignment: [TargetAlignment]
-    "Multiple sequence alignment of group members."
-    target_alignment_subset(after: String, first: Int!): TargetAlignmentConnection
-}
-
-type AnnotationFeatures {
-    "List of positional features"
-    features: [Feature]
-    "Enumerated value that identifies the provenance type of the positional features"
-    source: Source
-    "Database source entry identifier associated to the positional features"
-    target_id: String
-    target_identifiers: TargetIdentifiers
-}
-
-type Coverage {
-    "Percentage of the query sequence covered byt the alignment"
-    query_coverage: Int
-    "Length of the full query sequence"
-    query_length: Int
-    "Percentage of the target sequence covered byt the alignment"
-    target_coverage: Int
-    "Length of the full target sequence"
-    target_length: Int
-}
-
-type Feature {
-    additional_properties: [AdditionalProperty]
-    "Free-form text describing the feature"
-    description: String
-    "Identifier of the feature"
-    feature_id: String
-    " List of documents that describes the location of the feature"
-    feature_positions: [FeaturePosition]
-    "Name associated to the feature"
-    name: String
-    "Original database or software name used to obtain the feature"
-    provenance_source: String
-    """
-
-    The connection type.
-
-    Examples:
-    ASA_UNBOUND, BINDING_SITE, mutation, artifact, CATH, SCOP
-    """
-    type: Type
-    "Numerical value associated with the feature"
-    value: Float
-}
-
-type FeaturePosition {
-    "Index at which this segment of the feature begins on the original provenance_source. When reference and source point to the same reference system this file will be null"
-    beg_ori_id: Int
-    "Index at which this segment of the feature begins"
-    beg_seq_id: Int
-    "Index at which this segment of the feature ends on the original provenance_source. If the positional feature maps to a single residue this field will be null. When reference and source point to the same reference system this file will be null"
-    end_ori_id: Int
-    "Index at which this segment of the feature ends. If the positional feature maps to a single residue this field will be null"
-    end_seq_id: Int
-    "Flag that indicates the feature begins before the feature index begin"
-    open_begin: Boolean
-    "Flag that indicates the feature end after the feature index end"
-    open_end: Boolean
-    "Fragment identifier that groups a set of ranges resulting from gaps"
-    range_id: String
-    "The value for the feature at this region"
-    value: Float
-    "The value(s) for the feature at this region"
-    values: [Float]
-}
-
-"Information about pagination in a connection."
-type PageInfo {
-    "When paginating forwards, the cursor to continue."
-    endCursor: String
-    "When paginating forwards, are there more items?"
-    hasNextPage: Boolean!
-    "When paginating backwards, are there more items?"
-    hasPreviousPage: Boolean!
-    "When paginating backwards, the cursor to continue."
-    startCursor: String
-}
-
-"Query root"
-type Query {
-    "Get sequence alignments"
-    alignment(
-        "Query sequence database"
-        from: SequenceReference,
-        "Database sequence identifier"
-        queryId: String!,
-        "Optional integer list (2-tuple) to filter the alignments to a particular region"
-        range: [Int],
-        "Target Sequence database"
-        to: SequenceReference
-    ): AlignmentResponse
-    "Get positional features"
-    annotations(
-        "Optional list of filters that can be used to select what annotations will be retrieved"
-        filters: [FilterInput],
-        "Database entry for whom the annotations will be requested"
-        queryId: String!,
-        "Optional integer list (2-tuple) to filter annotations that fall in a particular region"
-        range: [Int],
-        "Query database"
-        reference: SequenceReference,
-        "List defining the annotation collections to be requested"
-        sources: [Source]
-    ): [AnnotationFeatures]
-    "Get group sequence alignments"
-    group_alignment(
-        "List of allowed PDB entities"
-        filter: [String],
-        "Group Type"
-        group: GroupReference!,
-        "Group Id"
-        groupId: String
-    ): AlignmentResponse
-    "Get group positional features"
-    group_annotations(
-        "Optional list of filters that can be used to select what annotations will be retrieved"
-        filters: [FilterInput],
-        "Group Type"
-        group: GroupReference!,
-        "Group Id"
-        groupId: String!,
-        "List defining the annotation collections to be requested"
-        histogram: Boolean,
-        "List defining the annotation collections to be requested"
-        sources: [Source]
-    ): [AnnotationFeatures]
-}
-
-type TargetAlignment {
-    "Aligned region"
-    aligned_regions: [AlignedRegion]
-    "Alignment scores"
-    coverage: Coverage
-    "integer that identifies the DNA strand of genome alignments (1 positive strand / -1 negative strand)"
-    orientation: Int
-    "Database identifier of the target"
-    target_id: String
-    "Full sequence of the target"
-    target_sequence: String
-}
-
-"A connection to a list of items."
-type TargetAlignmentConnection {
-    "a list of edges"
-    edges: [TargetAlignmentEdge]
-    "details about this specific page"
-    pageInfo: PageInfo!
-}
-
-"An edge in a connection"
-type TargetAlignmentEdge {
-    "cursor marks a unique position or index into the connection"
-    cursor: String!
-    "The item at the end of the edge"
-    node: TargetAlignment
-}
-
-type TargetIdentifiers {
-    assembly_id: String
-    asym_id: String
-    entity_id: String
-    entry_id: String
-    interface_id: String
-    interface_partner_index: Int
-    target_id: String
-    uniprot_id: String
-}
-
-enum GroupReference {
-    matching_uniprot_accession
-    sequence_identity
-}
-
-enum PropertyName {
-    CARD_MODEL_DESCRIPTION
-    CARD_MODEL_ORGANISM
-    CATH_DOMAIN_ID
-    CATH_NAME
-    CLINICAL_SIGNIFICANCE
-    CONSEQUENCE_TYPE
-    DISEASE_TYPE
-    ECOD_DOMAIN_ID
-    ECOD_FAMILY_NAME
-    EVIDENCE
-    LINK
-    MODELCIF_MODEL_ID
-    MUTATED_TYPE
-    OMEGA_ANGLE
-    PARENT_COMP_ID
-    PARTNER_ASYM_ID
-    PARTNER_BOND_DISTANCE
-    PARTNER_COMP_ID
-    PREDICTED_IMPACT
-    SCOP_2_DOMAIN_ID
-    SCOP_2_FAMILY_ID
-    SCOP_2_FAMILY_NAME
-    SCOP_2_SUPERFAMILY_ID
-    SCOP_2_SUPERFAMILY_NAME
-    SCOP_DOMAIN_ID
-    SCOP_NAME
-    SCOP_SUN_ID
-    SHEET_SENSE
-    STRAIN_ID
-    SUBTYPE
-    WILD_TYPE
-}
-
-enum SequenceReference {
-    NCBI_GENOME
-    NCBI_PROTEIN
-    PDB_ENTITY
-    PDB_INSTANCE
-    UNIPROT
-}
-
-enum Source {
-    PDB_ENTITY
-    PDB_INSTANCE
-    PDB_INTERFACE
-    UNIPROT
-}
-
-enum Type {
-    ACTIVE_SITE
-    ANGLE_OUTLIER
-    ARTIFACT
-    ASA
-    ASA_BOUND
-    ASA_UNBOUND
-    BEND
-    BINDING_SITE
-    BOND_OUTLIER
-    CALCIUM_BINDING_REGION
-    CARD_MODEL
-    CATH
-    CHAIN
-    CIS_PEPTIDE
-    COMPOSITIONALLY_BIASED_REGION
-    COVALENT_BOND
-    COVALENT_MODIFICATION_OF_A_NUCLEOTIDE_BASE
-    COVALENT_MODIFICATION_OF_A_NUCLEOTIDE_PHOSPHATE
-    COVALENT_MODIFICATION_OF_A_NUCLEOTIDE_SUGAR
-    COVALENT_RESIDUE_MODIFICATION
-    CROSS_LINK
-    C_MANNOSYLATION_SITE
-    DISORDER
-    DISORDER_BINDING
-    DISULFIDE_BRIDGE
-    DNA_BINDING_REGION
-    DOMAIN
-    ECOD
-    GLYCOSYLATION_SITE
-    HELIX_P
-    HELX_LH_PP_P
-    HELX_RH_3_T_P
-    HELX_RH_AL_P
-    HELX_RH_PI_P
-    HYDROGEN_BOND
-    HYDROPATHY
-    IMGT_ANTIBODY_DESCRIPTION
-    IMGT_ANTIBODY_DOMAIN_NAME
-    IMGT_ANTIBODY_GENE_ALLELE_NAME
-    IMGT_ANTIBODY_ORGANISM_NAME
-    IMGT_ANTIBODY_PROTEIN_NAME
-    IMGT_ANTIBODY_RECEPTOR_DESCRIPTION
-    IMGT_ANTIBODY_RECEPTOR_TYPE
-    INITIATOR_METHIONINE
-    INTRAMEMBRANE_REGION
-    IONIC_INTERACTION
-    LIPID_MOIETY_BINDING_REGION
-    MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY
-    MA_QA_METRIC_LOCAL_TYPE_DISTANCE
-    MA_QA_METRIC_LOCAL_TYPE_ENERGY
-    MA_QA_METRIC_LOCAL_TYPE_IPTM
-    MA_QA_METRIC_LOCAL_TYPE_NORMALIZED_SCORE
-    MA_QA_METRIC_LOCAL_TYPE_OTHER
-    MA_QA_METRIC_LOCAL_TYPE_PAE
-    MA_QA_METRIC_LOCAL_TYPE_PLDDT
-    MA_QA_METRIC_LOCAL_TYPE_PLDDT_0_1
-    MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL_ATOM
-    MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL_ATOM_0_1
-    MA_QA_METRIC_LOCAL_TYPE_PTM
-    MA_QA_METRIC_LOCAL_TYPE_ZSCORE
-    MEMBRANE_SEGMENT
-    METAL_COORDINATION
-    METAL_ION_BINDING_SITE
-    MISMATCHED_BASE_PAIRS
-    MODIFIED_MONOMER
-    MODIFIED_RESIDUE
-    MOGUL_ANGLE_OUTLIER
-    MOGUL_BOND_OUTLIER
-    MUTAGENESIS_SITE
-    MUTATION
-    NON_CONSECUTIVE_RESIDUES
-    NON_STANDARD_AMINO_ACID
-    NON_TERMINAL_RESIDUE
-    NUCLEOTIDE_PHOSPHATE_BINDING_REGION
-    N_GLYCOSYLATION_SITE
-    O_GLYCOSYLATION_SITE
-    PEPTIDE
-    PFAM
-    PROPEPTIDE
-    PROTEIN_BINDING
-    RAMACHANDRAN_OUTLIER
-    REGION_OF_INTEREST
-    REPEAT
-    ROTAMER_OUTLIER
-    RSCC_OUTLIER
-    RSRZ_OUTLIER
-    SABDAB_ANTIBODY_ANTIGEN_NAME
-    SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS
-    SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS
-    SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE
-    SABDAB_ANTIBODY_NAME
-    SABDAB_ANTIBODY_TARGET
-    SCOP
-    SCOP_2_B_SUPERFAMILY
-    SCOP_2_FAMILY
-    SCOP_2_SUPERFAMILY
-    SEQUENCE_CONFLICT
-    SEQUENCE_VARIANT
-    SHEET
-    SHORT_SEQUENCE_MOTIF
-    SIGNAL_PEPTIDE
-    SITE
-    SPLICE_VARIANT
-    STEREO_OUTLIER
-    STRN
-    S_GLYCOSYLATION_SITE
-    TOPOLOGICAL_DOMAIN
-    TRANSIT_PEPTIDE
-    TRANSMEMBRANE_REGION
-    TURN_TY_1_P
-    UNASSIGNED_SEC_STRUCT
-    UNOBSERVED_ATOM_XYZ
-    UNOBSERVED_RESIDUE_XYZ
-    UNSURE_RESIDUE
-    ZERO_OCCUPANCY_ATOM_XYZ
-    ZERO_OCCUPANCY_RESIDUE_XYZ
-    ZINC_FINGER_REGION
-}
-
-enum fieldName {
-    target_id
-    type
-}
-
-enum operationType {
-    contains
-    equals
-}
-
-"Built-in scalar for dynamic values"
-scalar ObjectScalar
-
-"Use SPQR's SchemaPrinter to remove this from SDL"
-scalar UNREPRESENTABLE
-
-input FilterInput {
-    field: fieldName
-    operation: operationType
-    source: Source
-    values: [String]
-}

package/lib/commonjs/RcsbQueries/QueryCheck.d.ts

@@ -1 +0,0 @@
-export {};

package/lib/commonjs/RcsbQueries/QueryCheck.js

@@ -1,20 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const tslib_1 = require("tslib");
-const configBorregoGraphQL = tslib_1.__importStar(require("../RcsbServerConfig/codegen.borrego.json"));
-const configYosemiteGraphQL = tslib_1.__importStar(require("../RcsbServerConfig/codegen.yosemite.json"));
-const GeneratorTools_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Generator/GeneratorTools");
-console.info("Testing DATA API");
-(0, GeneratorTools_1.validateQueries)(configYosemiteGraphQL.schema, configYosemiteGraphQL.documents).then(() => {
-    console.log("DATA API request OK");
-    console.info("Testing 1D API");
-    (0, GeneratorTools_1.validateQueries)(configBorregoGraphQL.schema, configBorregoGraphQL.documents).then(() => {
-        console.log("1D API request OK");
-    }).catch(e => {
-        console.error("1D API failed");
-        console.error(e);
-    });
-}).catch(e => {
-    console.error("DATA API failed");
-    console.error(e);
-});

package/lib/commonjs/RcsbQueries/Yosemite/.graphqlconfig

@@ -1,15 +0,0 @@
-{
-  "name": "Untitled GraphQL Schema",
-  "schemaPath": "schema.graphql",
-  "extensions": {
-    "endpoints": {
-      "Default GraphQL Endpoint": {
-        "url": "https://data.rcsb.org/graphql",
-        "headers": {
-          "user-agent": "JS GraphQL"
-        },
-        "introspect": false
-      }
-    }
-  }
-}

package/lib/commonjs/RcsbQueries/Yosemite/QueryAssemblyInterfaces.graphql

@@ -1,10 +0,0 @@
-query QueryAssemblyInterfaces($assembly_ids: [String!]!){
-    assemblies(
-        assembly_ids: $assembly_ids
-    ){
-        rcsb_id
-        interfaces{
-            rcsb_id
-        }
-    }
-}

package/lib/commonjs/RcsbQueries/Yosemite/QueryEntryInstances.graphql

@@ -1,51 +0,0 @@
-query QueryEntryInstance($entry_id: String!){
-    entry(
-        entry_id:$entry_id
-    ){
-        polymer_entities {
-            polymer_entity_instances{
-                rcsb_id
-                polymer_entity{
-                    rcsb_polymer_entity{
-                        pdbx_description
-                        rcsb_polymer_name_combined{
-                            names
-                        }
-                        formula_weight
-                    }
-                    entity_poly{
-                        rcsb_entity_polymer_type
-                        rcsb_sample_sequence_length
-                    }
-                    rcsb_entity_source_organism {
-                        ncbi_scientific_name
-                    }
-                    entry {
-                        rcsb_entry_info{
-                            experimental_method
-                            resolution_combined
-                            molecular_weight
-                            structure_determination_methodology
-                        }
-                    }
-                }
-                rcsb_polymer_entity_instance_container_identifiers{
-                    asym_id
-                    auth_asym_id
-                    entry_id
-                    entity_id
-                    auth_to_entity_poly_seq_mapping
-                }
-            }
-        }
-        assemblies {
-            rcsb_assembly_container_identifiers {
-                assembly_id
-            }
-            pdbx_struct_assembly_gen{
-                asym_id_list
-            }
-
-        }
-    }
-}

package/lib/commonjs/RcsbQueries/Yosemite/QueryGroup.graphql

@@ -1,15 +0,0 @@
-query QueryGroup($group_id: String!){
-    polymer_entity_group(
-        group_id:$group_id
-    ){
-        rcsb_id
-        rcsb_group_info{
-            group_name
-            group_description
-            group_members_granularity
-        }
-        rcsb_group_container_identifiers{
-            group_member_ids
-        }
-    }
-}

package/lib/commonjs/RcsbQueries/Yosemite/QueryInterfaceInstances.graphql

@@ -1,18 +0,0 @@
-query QueryInterfaceInstance($interface_ids: [String!]!){
-    interfaces(
-        interface_ids:$interface_ids
-    ){
-        rcsb_interface_container_identifiers{
-            rcsb_id
-            interface_id
-            assembly_id
-            entry_id
-        }
-        rcsb_interface_partner{
-            interface_partner_identifier{
-                asym_id
-            }
-        }
-        rcsb_interface_operator
-    }
-}

package/lib/commonjs/RcsbQueries/Yosemite/QueryMultipleEntityInstances.graphql

@@ -1,39 +0,0 @@
-query QueryMultipleEntityInstances($entity_ids: [String!]!){
-    polymer_entities(
-        entity_ids:$entity_ids
-    ){
-        polymer_entity_instances{
-            rcsb_id
-            polymer_entity{
-                rcsb_polymer_entity{
-                    pdbx_description
-                    rcsb_polymer_name_combined{
-                        names
-                    }
-                    formula_weight
-                }
-                entity_poly{
-                    rcsb_entity_polymer_type
-                    rcsb_sample_sequence_length
-                }
-                rcsb_entity_source_organism {
-                    ncbi_scientific_name
-                }
-                entry {
-                    rcsb_entry_info{
-                        experimental_method
-                        resolution_combined
-                        structure_determination_methodology
-                    }
-                }
-            }
-            rcsb_polymer_entity_instance_container_identifiers{
-                asym_id
-                auth_asym_id
-                entry_id
-                entity_id
-                auth_to_entity_poly_seq_mapping
-            }
-        }
-    }
-}

package/lib/commonjs/RcsbQueries/Yosemite/QueryMultipleEntriesProperties.graphql

@@ -1,53 +0,0 @@
-query multiple_entries_properties($entry_ids: [String!]!){
-    entries(entry_ids:$entry_ids){
-        rcsb_id
-        polymer_entities {
-            rcsb_id
-            rcsb_entity_source_organism {
-                ncbi_scientific_name
-            }
-            rcsb_polymer_entity_container_identifiers {
-                entity_id
-                rcsb_id
-            }
-            polymer_entity_instances {
-                rcsb_polymer_entity_instance_container_identifiers {
-                    asym_id
-                }
-                rcsb_id
-            }
-            entity_poly {
-                rcsb_prd_id
-            }
-        }
-        nonpolymer_entities {
-            rcsb_id
-            rcsb_nonpolymer_entity_container_identifiers {
-                entity_id
-                rcsb_id
-            }
-            nonpolymer_entity_instances {
-                rcsb_nonpolymer_entity_instance_container_identifiers {
-                    asym_id
-                }
-                rcsb_id
-            }
-        }
-        rcsb_entry_info{
-            experimental_method
-            resolution_combined
-            molecular_weight
-            structure_determination_methodology
-        }
-        struct {
-            title
-        }
-        assemblies {
-            rcsb_id
-            pdbx_struct_assembly_gen {
-                oper_expression
-                asym_id_list
-            }
-        }
-    }
-}

package/lib/commonjs/RcsbQueries/Yosemite/QueryMultipleInstanceSequences.graphql

@@ -1,11 +0,0 @@
-
-query multiple_instance_sequences($instance_ids: [String!]!){
-    polymer_entity_instances(instance_ids:$instance_ids){
-        rcsb_id
-        polymer_entity{
-            entity_poly{
-                pdbx_seq_one_letter_code_can
-            }
-        }
-    }
-}